BACKGROUND: Rotavirus is the most important aetiological agent causing severe gastroenteritis in children <2 years of age in South Africa and worldwide. Most endemic neonatal nursery strains are thought to be asymptomatic. However, serious conditions have been reported to be associated with rotavirus infection, such as necrotising enterocolitis (NEC), diffuse intravascular coagulopathy, pneumonia, apnoea and seizures. METHODS: We studied newborns needing screening for sepsis in our Neonatal Unit. Rotavirus screening was included in the septic screen. The clinical signs and symptoms were studied in the control group (no rotavirus identified) and the study group (rotavirus identified in the stools). RESULTS: Of the 169 babies screened for sepsis, 44 (26%) were rotavirus positive. Of the remainder, 63 comprised the control group. Rotavirus-positive stools were identified from day 4 of life. The virus was excreted in the stools for a mean of 4 days per infection episode. Asymptomatic infection was only observed in one baby; the others had clinical signs and symptoms ranging from mild to severe, and there were even some deaths. Gastrointestinal symptoms were prominent manifestations of rotavirus infection. There was a high incidence of NEC (66% in the study group v. 30% in the control group). Of the rotavirus-infected babies, 9 died; 3 had no other pathogens identified, so that rotavirus infection could have been the cause of death. CONCLUSIONS: Rotavirus infection in the neonate is rarely asymptomatic. It is a dangerous condition that may cause death. It is associated with, and probably a cause of, NEC.